--- a/bam_to_scidx.xml	Wed Jun 15 10:50:24 2016 -0400
+++ b/bam_to_scidx.xml	Wed Jun 22 09:46:19 2016 -0400
@@ -13,8 +13,9 @@
     </stdio>
     <command>
         <![CDATA[
-            ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
-            java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
+            ln -s "${input_bam}" "localbam.bam" &&
+            ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
+            java -jar $__tool_directory__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
         ]]>
     </command>
     <inputs>